default_layoutpolicy.cpp

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/*
 * ===========================================================================
 * PRODUCTION $Log: default_layoutpolicy.cpp,v $
 * PRODUCTION Revision 1000.3  2004/06/01 21:12:29  gouriano
 * PRODUCTION PRODUCTION: UPGRADED [GCC34_MSVC7] Dev-tree R1.13
 * PRODUCTION
 * ===========================================================================
 */

/*  $Id: default_layoutpolicy.cpp,v 1000.3 2004/06/01 21:12:29 gouriano Exp $
 * ===========================================================================
 *
 *                            PUBLIC DOMAIN NOTICE
 *               National Center for Biotechnology Information
 *
 *  This software/database is a "United States Government Work" under the
 *  terms of the United States Copyright Act.  It was written as part of
 *  the author's official duties as a United States Government employee and
 *  thus cannot be copyrighted.  This software/database is freely available
 *  to the public for use. The National Library of Medicine and the U.S.
 *  Government have not placed any restriction on its use or reproduction.
 *
 *  Although all reasonable efforts have been taken to ensure the accuracy
 *  and reliability of the software and data, the NLM and the U.S.
 *  Government do not and cannot warrant the performance or results that
 *  may be obtained by using this software or data. The NLM and the U.S.
 *  Government disclaim all warranties, express or implied, including
 *  warranties of performance, merchantability or fitness for any particular
 *  purpose.
 *
 *  Please cite the author in any work or product based on this material.
 *
 * ===========================================================================
 *
 * Authors:  Vlad Lebedev
 *
 * File Description:
 *
 */


#include <ncbi_pch.hpp>
#include <gui/widgets/seq_graphic/default_layoutpolicy.hpp>
#include <gui/config/feat_config_list.hpp>
#include <gui/objutils/feature.hpp>
#include <gui/objutils/alignment.hpp>
#include <gui/objutils/graph.hpp>
#include <gui/objutils/prot_product.hpp>
#include <gui/objutils/histogram.hpp>
#include <gui/objutils/utils.hpp>
#include <gui/objutils/seq_map.hpp>
#include <gui/objutils/comment.hpp>
#include <gui/objutils/sequence.hpp>

#include <objmgr/seq_vector.hpp>

BEGIN_NCBI_SCOPE
USING_SCOPE(objects);



const int kLabelsColWidth     = 100;  // width of a column small


CDefaultLayoutPolicy::CDefaultLayoutPolicy()
{
}


void CDefaultLayoutPolicy::SetHandle(const CBioseq_Handle& handle)
{
    m_Handle = handle;
}


void CDefaultLayoutPolicy::SetConfig(CSeqGraphicConfig* config)
{
    m_ConfigSettings = config;
}


void CDefaultLayoutPolicy::PrepareData(CGlPane& pane, CLayout& lay_objects)
{
    pane.OpenOrtho();

    if (x_IsOverviewMode(pane)) {
        x_PrepareGenesOverview(pane, lay_objects);
    } else {
        x_PrepareDetailedView(pane, lay_objects);
    }

    pane.Close();
}


bool CDefaultLayoutPolicy::x_IsOverviewMode(CGlPane& pane) const
{
    TModelRect rcV  = pane.GetVisibleRect();
    TSeqRange range( TSeqPos(rcV.Left()), TSeqPos(rcV.Right()) );

    TModelUnit scale = pane.GetScaleX();    
    
    TSeqPos over_cut_off = m_ConfigSettings->GetOverviewCutoff();
    TSeqPos gene_cut_off = m_ConfigSettings->GetGenesCutoff();
    
    SAnnotSelector sel = CSeqUtils::GetAnnotSelector(CSeqFeatData::e_Gene);
    CFeat_CI iter(m_Handle, range.GetFrom(), range.GetTo(), sel);

    return scale > over_cut_off  &&  iter.GetSize() > gene_cut_off;
}


void CDefaultLayoutPolicy::x_PrepareGenesOverview(CGlPane& pane, CLayout& lay_objects)
{
    TModelRect rcV = pane.GetVisibleRect();
    TSeqRange range( TSeqPos(rcV.Left()), TSeqPos(rcV.Right()) );

    C2DLayoutEngine engine;
    engine.SetMinDist( x_GetMinSpacing(pane) );

    CLayout temporary;
    CLayoutEngine::TObjects objs, obj_tmp;
    CLayoutFeatLabel::TFeatLabelList marks_labels;
    
    lay_objects.Clear();
    engine.Layout(objs, lay_objects);
    
    // Add segment map
    if (m_ConfigSettings->GetShowSegmentMap()) {  // add Segment map
        x_AddSeqSegmentMap(pane, lay_objects, range);
    }
    
    x_AddHistograms(pane, lay_objects, range);
    
    // retrieve landmark features first
    CLayoutFeat::TFeatList land_marks;
    CSeqUtils::GetLandmarkFeatures(m_Handle, range, 200, land_marks);

    // Comments for All Genes
    string str2 = "Only Landmark Genes Shown: " + NStr::UIntToString(land_marks.size());
    CRef<CLayoutObject> comment(new CLayoutComment(str2));
    objs.push_back(comment);
    engine.Layout(objs, temporary);
    lay_objects.Append(temporary);

    // we need to assemble a slightly different structure first
    objs.clear();
    NON_CONST_ITERATE (CLayoutFeat::TFeatList, iter, land_marks) {
        CLayoutFeat& feat = **iter;
        CRef<CLayoutFeatLabel> lbl
            (new CLayoutFeatLabel(feat.GetMappedFeature()));

        CRef<CLayoutObject> obj(*iter);

        marks_labels.push_back(lbl);  // store for sorting
        objs.push_back(obj);
    }


    engine.Layout(objs, temporary);
    lay_objects.Append(temporary);

    x_AddFeatureLabelsOverview(marks_labels, pane, lay_objects);
}


void CDefaultLayoutPolicy::x_AddHistograms(CGlPane& pane, 
            CLayout& lay_objects, TSeqRange range)
{
    CLayoutEngine::TObjects objs;
    CLayout temp;
    C2DLayoutEngine engine;
    
    // Show histograms first
    ITERATE(CFeatConfigList, iter, *GetFeatConfigList()) {
        bool hist = m_ConfigSettings->GetHistogram(iter->GetType(), iter->GetSubtype());
        if(!hist) continue;
                
        SAnnotSelector selector = CSeqUtils::GetAnnotSelector
            (CSeqFeatData::ESubtype(iter->GetSubtype()) );
                            
        selector.SetSortOrder(SAnnotSelector::eSortOrder_None);
        CDensityMap<int> densityMap(range.GetFrom(), range.GetTo(),
                                    TSeqPos(pane.GetScaleX()));
        densityMap.AddFeatures(m_Handle, selector);
        
        if (densityMap.GetBins() == 0) { // skip empty maps
            continue;
        }
        CRef<CLayoutObject> dmap(new CLayoutHistogram(densityMap, 
                                CSeqFeatData::E_Choice(iter->GetType()), 
                                CSeqFeatData::ESubtype(iter->GetSubtype())) );
        objs.push_back(dmap);
    }
    
    engine.Layout(objs, temp);
    lay_objects.Append(temp);
}


void CDefaultLayoutPolicy::x_AddFeatureLabelsOverview(
                CLayoutFeatLabel::TFeatLabelList& labels, 
                CGlPane& pane, CLayout& lay_objects)
{
    // sort feature labels alphabetically
    sort(labels.begin(), labels.end(), SFeatureByName());

    // a number of columns that will fit
    int cols_count = pane.GetViewport().Width() / kLabelsColWidth;
        
    if (cols_count == 0) {
        cols_count = 1; // always at least 1 column
    }

    // assign columns and repack
    int cur_col = 0;
    CLayoutEngine::TObjects labels_obj;
    NON_CONST_ITERATE (CLayoutFeatLabel::TFeatLabelList, iter, labels) {
        (*iter)->SetColumn(cur_col);  // set the column index
        CRef<CLayoutObject> obj(*iter);
        labels_obj.push_back(obj);

        if (++cur_col >= cols_count) {
            cur_col = 0;
        }
    }

    CLayout labels_layout;
    x_LayoutLabels(labels_obj, labels_layout, cols_count);
    lay_objects.Append(labels_layout);    
}


void CDefaultLayoutPolicy::
x_AddSequenceBar(CGlPane& pane, CLayout& lay_objects, TSeqRange range)
{
    if (pane.GetScaleX() > 1.0f / 8.0f ) { // sequence would not fit
        return;
    }
    
    CLayout temp;
    C2DLayoutEngine engine;
    CLayoutEngine::TObjects obj_tmp;
    
    string seq_str;
    CSeqVector s_vec = m_Handle.GetSeqVector(CBioseq_Handle::eCoding_Iupac);
    s_vec.GetSeqData(range.GetFrom(), range.GetTo(), seq_str);
    
    CRef<CLayoutObject> sequence(new CLayoutSequence(seq_str));

    // Add to layout
    obj_tmp.push_back(sequence);
    engine.Layout(obj_tmp, temp);
    lay_objects.Append(temp);
}


void CDefaultLayoutPolicy::x_AddSeqSegmentMap(CGlPane& pane, CLayout& lay_objects, TSeqRange range)
{
    CLayoutEngine::TObjects objs, obj_tmp;
    
    // Segment maps first
    GetSeqMaps(objs, range);
    
    // Do not do anything if no segments
    if (objs.size() == 0) {
        return;
    }
    
    string str = "Segment Map: " + NStr::UIntToString(objs.size());
    CRef<CLayoutObject> comment(new CLayoutComment(str));

    C2DLayoutEngine engine;
    engine.SetMinDist(x_GetMinSpacing(pane) );
 
    CLayout temp, temp2;   
    obj_tmp.push_back(comment);
    engine.Layout(obj_tmp, temp);
    lay_objects.Append(temp);
    engine.Layout(objs, temp2);
    
    unsigned int kMaxSegMapRows = 4; // no more than 4 rows
    for (size_t idx = 0; idx != temp2.GetLayout().size()  &&  
                                idx < kMaxSegMapRows; idx++) {